mkrangi.sh

   1 # create RANGI input files for protein interaction networks
   2 if [ $# != 5 ]
   3 then
   4         echo "Create RANGI input files for protein interaction networks"
   5         echo
   6         echo "Usage: mkrangi.sh NET FASN FASP CMPL PRE"
   7         echo
   8         echo "  NET: the network interaction file"
   9         echo "  FASN: network fasta file"
  10         echo "  FASP: pattern fasta file"
  11         echo "  CMPL: pattern complexes (queries)"
  12         echo "  PRE: output file prefix"
  13         echo
  14         echo "Output files will be written to PRE.i.rangi, where i is"
  15         echo "replaced with the line number of the query in CMPL.  Note"
  16         echo "that you need the blast program."
  17         echo
  18         echo "The necessary files can be obtained from:"
  19         echo "http://igm.univ-mlv.fr/AlgoB/gramofone/"
  20         exit
  21 fi
  22
  23 # parameters
  24 NET="$1"
  25 FASN="$2"
  26 FASP="$3"
  27 CMPL="$4"
  28 PRE="$5"
  29
  30 # temporary files
  31 FASP2=${FASP}_
  32 QBL=${NET}_
  33
  34 cat $CMPL | cut -f 2 | tr ' ' '\n' | sed '/^\s\+$/d' | sort | uniq | ./fastafilt $FASP >$FASP2
  35 formatdb -p T -i $FASN
  36 formatdb -p T -i $FASP2
  37 blastall -p blastp -i $FASP2 -d $FASN | ./bl2exp >$QBL
  38
  39 id=0
  40 cat $CMPL | cut -f 2 | while read k
  41 do
  42         id=$(( $id + 1 ))
  43         DAT="$PRE.$id.rangi"
  44         DATG="$PRE.$id.dot"
  45         ./conv -q $QBL $k <$NET >$DAT
  46         ./conv -g -q $QBL $k <$NET >$DATG
  47 done
  48
  49 rm $FASP2 $QBL